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- PDB-8tct: Structure of 3K-GlcH bound Bacteroides thetaiotaomicron 3-Keto-be... -

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Basic information

Entry
Database: PDB / ID: 8tct
TitleStructure of 3K-GlcH bound Bacteroides thetaiotaomicron 3-Keto-beta-glucopyranoside-1,2-Lyase BT1
ComponentsSugar phosphate isomerase/epimerase
KeywordsISOMERASE / Sugar Phosphate Isomerase
Function / homology: / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / isomerase activity / : / PHOSPHATE ION / : / Sugar phosphate isomerase/epimerase
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsLazarski, A.C. / Worrall, L.J. / Strynadka, N.C.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Nature / Year: 2024
Title: An alternative broad-specificity pathway for glycan breakdown in bacteria.
Authors: Nasseri, S.A. / Lazarski, A.C. / Lemmer, I.L. / Zhang, C.Y. / Brencher, E. / Chen, H.M. / Sim, L. / Panwar, D. / Betschart, L. / Worrall, L.J. / Brumer, H. / Strynadka, N.C.J. / Withers, S.G.
History
DepositionJul 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Sugar phosphate isomerase/epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0789
Polymers33,2871
Non-polymers7918
Water3,873215
1
A: Sugar phosphate isomerase/epimerase
hetero molecules

A: Sugar phosphate isomerase/epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,15518
Polymers66,5742
Non-polymers1,58216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area3830 Å2
ΔGint-65 kcal/mol
Surface area22320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.287, 122.287, 68.747
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-589-

HOH

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Components

#1: Protein Sugar phosphate isomerase/epimerase


Mass: 33286.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BT_2156 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A5T2
#2: Chemical ChemComp-UC6 / 1,5-anhydro-D-ribo-hex-3-ulose


Mass: 162.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.46 Å3/Da / Density % sol: 72.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 27% PEG 300 0.11 M Phosphate Citrate pH 4.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.1807 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1807 Å / Relative weight: 1
ReflectionResolution: 1.86→45.69 Å / Num. obs: 49947 / % possible obs: 99.93 % / Redundancy: 19.9 % / CC1/2: 1 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.026 / Rrim(I) all: 0.085 / Net I/σ(I): 26.9
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 20 % / Rmerge(I) obs: 2.902 / Num. unique obs: 4903 / CC1/2: 0.619 / Rpim(I) all: 0.951 / Rrim(I) all: 3.056

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→45.69 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1829 --
Rwork0.1679 --
obs-49947 99.93 %
Refinement stepCycle: LAST / Resolution: 1.86→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 42 215 2474

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